The macroviruses, Dr. Chaotica, and Seska hinder Chakotay and Janeway's attempt to restore Voyager to its normal state after a temporal distortion shifts sections of the ship into different timeframes.

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USS Voyager goes through a temporal rift and the ship is shattered into 37 different timeframes. Chakotay is injured by a bolt from the overloaded warp core. He's beamed to sickbay, where The Doctor injects him with a chroniton-infused serum which allows him to travel between the different timeframes. He goes to the bridge and selects CaptainJaneway as his ally. In this timeframe, Janeway only knows of him as a leader of the Maquis cell she was ordered to capture. Despite her protests, Chakotay injects her with the chroniton serum created by The Doctor. Together, they travel through the different timeframes in order to restore the ship to the proper timeline.

Chakotay enters the cargo bay where he finds Naomi Wildman and Icheb working on an educational jigsaw puzzle. Chakotay is in a bit of a hurry, looking for his stash of Antarian cider. He wants to bring a bottle to his weekly dinner with Captain Janeway. He is in a good mood and quite amused with Icheb's frustration with Naomi's playful attitude while she is supposed to be studying. He tells Icheb not to tell Neelix of his hiding place, as he only has a couple of bottles left. Icheb suggests to hide the cider among Borg spare parts, where Neelix is sure not to snoop.

While Chakotay and Captain Janeway enjoy a quiet dinner in the captain's quarters – or rather attempt to, since her replicator decides to burn her pot roast – Voyager encounters a temporal anomaly. Chakotay quickly runs down to engineering while the captain gets to the bridge.

In engineering, Chakotay tries to prevent a warp core breach, but a surge of temporal energy travels through the core, and hits him. He is quickly transported to sickbay showing signs of progeria on his face and in various organs of his body.

The Doctor develops a treatment for his condition, and Chakotay heads off to the bridge to find the captain after The Doctor informs him that he is not able to contact anyone else or leave sickbay. The Doctor has not heard of his mobile emitter.

Once in the turbolift, a strange wave of light sweeps from above as the lift rises to the bridge, and the medkit that he was carrying vanishes. When Chakotay arrives on the bridge, he causes a stir and Janeway acts as if she doesn't know him. The captain's long hair is tied up in bun, much like when Voyager arrived in the Delta Quadrant. Janeway informs him that Voyager is pursuing the Maquis ship in the Badlands, and that Chakotay is her primary target. She orders him taken to the brig, but the officers with him vanish as they go down in the turbolift, and he arrives in engineering during the Kazon takeover of Voyager by Seska. Chakotay manages to escape through another distortion. Seska asks the rest of the Kazon in Engineering to scan for anomalies.

Chakotay manages to get back to sickbay, where he realizes that The Doctor's treatment allows him to pass through the time distortions.

With this in mind, Chakotay takes a hypospray with the serum in it and heads back to the bridge, where he confronts the past Janeway once more. Chakotay tells her that an anomaly has hit the ship in the future causing him to shift into the past. Janeway tells him that her helmsman (assumed to be LieutenantStadi, although there is no official evidence of this) walked out of her ready room into the corridor and disappeared. However, the occurrence doesn't sway Janeway into believing Chakotay, so he claims the hypospray holds poison and presses it against Janeway's neck, threatening to kill her. Chakotay, still holding the captain, heads off in the direction that the crew member had gone before they disappeared. The two shift into another timeline, Chakotay having injected Janeway with the hypospray seconds earlier.

Chakotay explains to Janeway that it is all true and that they are good friends in the future. Still skeptical, Janeway offers her help in formulating a plan, but they must get to sickbay. On the way to sickbay, they pass into another timeframe, one where two wounded crew members are laying on the ground. Chakotay theorizes that it may be either the timeframe when Voyager was under the influence of the dream species or when Voyager encountered the telepathic pitcher plant. He assures Janeway that the crew will be fine.

A future Naomi Wildman

Chakotay suggests they go to astrometrics to scan the ship for temporal fractures, surprising Janeway who doesn't think Voyager has such a lab. They enter astrometrics to find Icheb and Naomi Wildman as adult Starfleet crewmembers, surprised to see them since, in their timeline, the captain and her first officer had died seventeen years earlier.

Icheb and Naomi reveal that the ship has been fractured into thirty-seven different timeframes. Naomi wishes that Seven of Nine was there to help them but tells Chakotay and Janeway that they don't know when or where she is.

They find her in Cargo Bay 2, still a pure Borg drone, with the other Borg drones that beamed aboard during their alliance. She informs them that the way that Borg vessels keep in temporal sync is by projecting a chroniton field and suggests that if they modify the bio-neural gel packs that run Voyager's systems, it will return Voyager to Chakotay's timeline.

The Doctor modifies a pair of bandoleers to resist the temporal barriers to hold the hyposprays. The Doctor starts talking about the Delta Quadrant, but Chakotay cuts him off, not wishing to violate the Temporal Prime Directive any more than Chakotay already had. Chakotay and Janeway head off to inject the necessary packs, first passing through time into past events, although Chakotay does not realize this at first. They inject the gel pack, and narrowly escape when a macrovirus turns up. It chases them through a time distortion and disappears.

They find themselves having enter the holodeck into Tom Paris' favorite holoprogram, Captain Proton, where they are met by the various cheesy characters that they must get past to inject the gelpack in holodeck number two, mainly achieved by Janeway's reluctant impersonation of Queen Arachnia.

Janeway is strapped to a table while Chaotica is preparing to torture her. Then Janeway and Chakotay tell Chaotica that there is a danger from the 8th dimension. Choatica is then manipulated into exposing and injecting the gelpack and they manage to convince him to release them to rid the rest of chaotica's realm of those gelpacks.

In the transporter room, they encounter several members of the Maquis, including B'Elanna Torres and Ayala. They are hostile to Janeway and Chakotay, but allow them to inject the gelpack and leave. Janeway questions Torres' comments about stranding them in the Delta Quadrant and Chakotay assures her that she did it for a good reason.

When they enter the mess hall, they find it being used as a sickbay and injured crewmen litter the floor, being treated by Tom Paris for radiation poisoning due to the temporal anomaly in Chakotay's timeline. Neelix gives Janeway some coffee, while Chakotay injects the gelpack. Janeway then finds a badly-injured Tuvok, who greets her before dying. In a turbolift Janeway hatches an alternative plan: to bring the entire Voyager into her timeframe. She discusses her plan with Chakotay, who dismisses it, telling her about some of the people that she's helped over the years, such as Paris and Torres' marriage. They leave discussing Seska.

She is in engineering, which is in the period that the Kazon took over the ship. She realizes that if Chakotay is there from the future, then they must have re-taken the ship from the Kazon and makes an attempt to bring the ship into sync with her timeframe.

Meanwhile Janeway, Paris and Kim watch from the higher section of engineering. Paris and Harry Kim leap onto two of the Kazon, while Naomi and Icheb correct the modification that Seska had already made. Ayala and B'Elanna Torres disarm another Kazon guard, but Seska holds Janeway hostage. She disarms Janeway and holds a weapon to her head, forcing all of them to drop their weapons. Seska is about to kill Janeway when Seven of Nine enters engineering, repelling Seska's shots with a Borg force field. She slaps Seska and chokes her, forcing her to release Janeway. This means that Chakotay can initiate the pulse, thus erasing the memories of the other participants while Chakotay averts the events that caused the anomaly.

Back in the present, Chakotay reminds Janeway that they have not finished their dinner. Janeway is surprised but follows Chakotay off the bridge. Back in her quarters, Janeway asks Chakotay about the experience. He declines to answer, gently reminding her of the Temporal Prime Directive. When they run out of cider, Janeway surprises Chakotay by suggesting he should go to the cargo bay to get another bottle. When Chakotay asks her how she found about it, Janeway also declines to answer, reminding him of the Temporal Prime Directive.

"There.""Excellent. You recognized the complementary base pair.""Actually, I just found two pieces that fit together.""You're missing the point.""I thought the point was to finish the puzzle.""And to learn something about genetics.""If you really want to help, find me a green piece that looks like Tuvok's ear."

- Naomi Wildman and Icheb working on a genetics puzzle

"Once, a long time ago, I called this replicator a glorified toaster. It never forgave me."

- Janeway, after burning yet another pot roast

"It's a fascinating story, but as the Ferengi say, a good lie is easier to believe than the truth."

- Janeway

"The Captain and I haven't risen from the grave."

- Chakotay

"Commander, in case you were wondering... I never told Neelix where you hid that cider."

"Your plan is inefficient."
"Why?"
"There are only two of you. If I were to assimilate you into a small Borg collective, you could then assimilate others. The work would proceed more quickly."
"Sorry, but I like my plan better. We'll be back."

- Seven of Nine and Janeway

"Doesn't sound like Mr. Paris' tastes are very sophisticated."
"That's why we love having him around."

"If Seven's idea works, Tuvok and those other crewmen will be fine."
"They'll still be stuck in the Delta Quadrant. If the temporal anomaly doesn't kill them something else will – the Borg, telepathic pitcher plants, macroviruses – the Delta Quadrant is a death trap!"
"What about the Temporal Prime Directive?"
"To hell with it!"

- Janeway (from 2371) and Chakotay, as the captain suggests realigning the ship with her timeframe to prevent Voyager from getting stuck in the Delta Quadrant

"That is not the future I have in mind."
"In that case... goodbye Chakotay."

- Chakotay and Seska

"I'd like to thank you now, for putting your doubts aside and helping me to put mine aside as well. Good luck to each of you."

- Janeway (from 2371), just before the timeline is restored

"For two people who started off as enemies, it seems to get to know each other pretty well, so I've been wondering... Just how close do we get?"
"Let's just say... there are some barriers we never cross."

- Janeway (from 2371) and Chakotay, as the captain wonders about the close friendship that she and Chakotay share

"Have you ever heard of a lightning rod? In about three seconds we're going to need one."

This episode is the last appearance of Doctor Chaotica (Martin Rayner) on the series. Robert Duncan McNeill was disappointed that he only appeared three times: "Personally, I would have liked to have done a lot more of Captain Proton. I think the studio and the producers felt like we had done it. We had reached such a pinnacle with it that to go back would be kind of doing it a disservice and undermining the specialness of the "Bride of Chaotica!" episode in particular. They were hesitant to go back for fear of ruining everyone's memories of it, but I would've loved it." (Star Trek: Voyager Companion). It is also the last appearance of Seska (Martha Hackett) and the Kazon.

This was the first original Star Trek episode to air in the 21st century (January 17, 2001). Filming of the episode took place from October 9-15, 2000. (StarTrek.com Production notes - The U.S.S. Voyager Gets "Shattered"wbm)